Problem Solved

Through trial and error I have managed to reolved the mirror and transparency error with the water. I have kept the same setting as before reguarding the components of the water. I discovered that the raytrace was the map causing the issue. I repaired this by going into the raytrace map, under the background settings clicked on non and added a water surface map. I then adjusted the colours of this map to a very light blue and white. From there I went back to the parent, and reduced the refraction settings from 100 to 45.

Maps in material editor

In the raytrace map

In the water surface map